Why my render is more noisy if MIS is on and sample rate is higher?
Some links to point you in the right direction:

Ways to get rid of fireflies (White pixels in your render)

Reduce noise in Cycles renders

The noise can be caused by a lot of factors and is a common issue with Cycles. 
I've personally found that Filter Glossy and increased clamping combined with more samples work best for me, but it's totally depending on your type of render. But I render a lot of glass myself, so I would assume this would work for you as well. But then again, check out the links I gave you for some good tips.